{"@attributes":{"version":"2.0"},"channel":{"title":"Joseph Szymborski has a blog.","link":"https:\/\/jszym.com\/","description":"Recent content on Joseph Szymborski has a blog.","generator":"Hugo -- gohugo.io","language":"en-ca","copyright":"This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.","lastBuildDate":"Mon, 11 Aug 2025 00:00:00 +0000","item":[{"title":"Where were you when goo.gl shutdown?","link":"https:\/\/jszym.com\/blog\/archiving_googl\/","pubDate":"Mon, 11 Aug 2025 00:00:00 +0000","guid":"https:\/\/jszym.com\/blog\/archiving_googl\/","description":""… all of this ended up in storage rooms, and everything became rotten and full of holes, and he himself finally turned into some kind of hole in humanity." \u272a\u272a“…\u0432\u0441\u0435 \u044d\u0442\u043e \u0441\u0432\u0430\u043b\u0438\u0432\u0430\u043b\u043e\u0441\u044c \u0432 \u043a\u043b\u0430\u0434\u043e\u0432\u044b\u0435, \u0438 \u0432\u0441\u0435 \u0441\u0442\u0430\u043d\u043e\u0432\u0438\u043b\u043e\u0441\u044c \u0433\u043d\u0438\u043b\u044c \u0438 \u043f\u0440\u043e\u0440\u0435\u0445\u0430, \u0438 \u0441\u0430\u043c \u043e\u043d \u043e\u0431\u0440\u0430\u0442\u0438\u043b\u0441\u044f \u043d\u0430\u043a\u043e\u043d\u0435\u0446 \u0432 \u043a\u0430\u043a\u0443\u044e-\u0442\u043e \u043f\u0440\u043e\u0440\u0435\u0445\u0443 \u043d\u0430 \u0447\u0435\u043b\u043e\u0432\u0435\u0447\u0435\u0441\u0442\u0432\u0435.”\n— Google Gogol, Dead Souls Vol. 1, Chp. 6\nIn December 2009, Google launched a URL shortening service alongside an update to their toolbar and FeedBurner."},{"title":"Visually Comparing Two PDFs Quickly","link":"https:\/\/jszym.com\/blog\/visually-comparing-pdfs\/","pubDate":"Mon, 12 May 2025 00:00:00 +0000","guid":"https:\/\/jszym.com\/blog\/visually-comparing-pdfs\/","description":"While I was preparing to submit my most recent manuscript, I had to quickly add line numbers. It just took a couple of lines in the LaTeX source file, but I was worried that doing so would subtley mess up the document in some way that I’d only realize after it was too late. To ensure that the two documents were identical but for the line numbers, I just overlayed them using pdftk and the following command:"},{"title":"Ending 20 Year Old Friendships using Genetic Algorithms","link":"https:\/\/jszym.com\/blog\/friendship-genetic-algo\/","pubDate":"Thu, 10 Apr 2025 00:00:00 +0000","guid":"https:\/\/jszym.com\/blog\/friendship-genetic-algo\/","description":"Prelude: Condorcet Voting It all started when some of my friends wanted to organize a hangout. Some of us have known each other for close to 20 years, and as we’ve grown older its been harder to find time to spend with one another, so when we do, we try to make it count.\nThat’s why, when trying to decide on a fun activity, there’s a little bit of pressure to make sure it’s something we’re all on board with."},{"title":"Hiding Images in XMP Metadata","link":"https:\/\/jszym.com\/blog\/xmp-steganography\/","pubDate":"Sat, 05 Oct 2024 00:00:00 +0000","guid":"https:\/\/jszym.com\/blog\/xmp-steganography\/","description":"I was avoiding getting out of bed when I came across a Mastodon post by @Foone that got me thinking. She had expressed a very reasonable thought, characteristic of her posts\u272a\u272aOk, for the most part. You should consider buying her a coffee, her feed is great., to include descriptions in the metadata of image so you wouldn’t have to write and rewrite alt texts every time you upload a file."},{"title":"Five Ways I Deal with Writer's Block","link":"https:\/\/jszym.com\/blog\/writers-block\/","pubDate":"Sun, 28 Apr 2024 00:00:00 +0000","guid":"https:\/\/jszym.com\/blog\/writers-block\/","description":"I never knew whether to think I’m an incredibly fast or a remarkably slow writer. Some days I can write pages and pages of scientific prose in a single sitting, and other days getting out a sentence or two is a major accomplishment. People in my life know better to ask me when I’ll be done writing something, as the answer is typically “I have no idea”.\nOver the years, though, I’ve developped a few coping mechanisms that work really well for me that I want to share."},{"title":"On Mastodon-powered Blog Comments","link":"https:\/\/jszym.com\/blog\/mastodon_blog_comments\/","pubDate":"Fri, 23 Feb 2024 00:00:20 -0500","guid":"https:\/\/jszym.com\/blog\/mastodon_blog_comments\/","description":"This is going to be a quick post, mostly spurred-on by @boris@cosocial.ca’s excellent suggestion.\nThis blog now has a comment section, and it’s powered by Mastodon, a federated micro-blog social network\u272a\u272aHere’s a 2 minute video introducing Mastodon if you have more questions..\nHow does it work? I make a post on cosocial.ca People can reply to the post. Those replies show up at the bottom of the corresponding blog post. Why’d you do that?"},{"title":"Maybe don't use Blake3 on Short Inputs","link":"https:\/\/jszym.com\/blog\/short_input_hash\/","pubDate":"Mon, 15 Jan 2024 00:00:20 -0500","guid":"https:\/\/jszym.com\/blog\/short_input_hash\/","description":"Motivation I have needs. Very specific needs. Namely, I want:\nTo hash a corpus of English words, individually …using a cryptographic hash …quickly …in Python. Putting aside that this is a strange thing to want to do, I’ve compiled a few benchmarks to help me chose the best function for my purposes. I’ve found plenty of benchmarks for all these hash functions, but they’re almost always for very large inputs."},{"title":"CSHL 2023 NetBio - Out-of-distribution multi-organism protein-protein interaction prediction for peptide therapeutics","link":"https:\/\/jszym.com\/meetings\/2023_cshl\/","pubDate":"Wed, 01 Mar 2023 00:00:00 +0000","guid":"https:\/\/jszym.com\/meetings\/2023_cshl\/","description":"Poster Download the poster we presented at CSHL 2023 here: \u21d3 poster.pdf (1.6 MB)\nPoster References Park Y, Marcotte EM. Flaws in evaluation schemes for pair-input computational predictions. Nat Methods. 2012 Dec;9(12):1134\u20136. DOI: 10.1038\/nmeth.2259 Merity S, Keskar NS, Socher R. Regularizing and Optimizing LSTM Language Models. arXiv:170802182 [cs] [Internet]. 2017 Aug 7 [cited 2021 Aug 10]; Available from: http:\/\/arxiv.org\/abs\/1708.02182 Szymborski J, Emad A. RAPPPID: towards generalizable protein interaction prediction with AWD-LSTM twin networks."},{"title":"ISMB 2022 - Improving Protein Interaction Prediction on Unseen Proteins","link":"https:\/\/jszym.com\/meetings\/2022_ismb\/","pubDate":"Tue, 05 Jul 2022 00:00:00 +0000","guid":"https:\/\/jszym.com\/meetings\/2022_ismb\/","description":"Presentation A pre-recorded version of this presentation can be downloaded here:\n\u25b6 rapppid_1080p.webm (125 MB)\n\u25b6 rapppid_720p.webm (64 MB)\n\u25b6 rapppid_480p.webm (33 MB)\nYou can download the slides in PDF format here:\n\u21d3 2022_ISMB_RAPPPID.pdf (9 MB)\nPoster You can download the poster we presented at ISMB 2022 here: \u21d3 poster.pdf (3 MB)\nManuscript You can find our paper published at OUP Bioinformatics:\nSzymborski J, Emad A. RAPPPID: Towards Generalisable Protein Interaction Prediction with AWD-LSTM Twin Networks."},{"title":"BIRS 2022 - Improving Protein Interaction Prediction on Unseen Proteins","link":"https:\/\/jszym.com\/meetings\/2022_birs\/","pubDate":"Sat, 28 May 2022 00:00:00 +0000","guid":"https:\/\/jszym.com\/meetings\/2022_birs\/","description":"Presentation You can preview the presentation on Speakerdeck.com.\nYou can also download the slides in PDF format here:\n\u21d3 2022_BIRS_RAPPPID.pdf (19.5 MB)\nA recording of the presentation can be viewed on the BIRS website or downloaded from here:\n\u25b6 2022_BIRS_RAPPPID.webm (52.4 MB)\nReferences You can find the references in this presentation within this Zotero Web Collection. You can also download them in BibTeX format: \u21d3 references.bib (8.7 KB)."}]}}